|
| Status |
Public on Oct 16, 2012 |
| Title |
U2OS.NT.input |
| Sample type |
SRA |
| |
|
| Source name |
U2OS_NT_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: human osteosarcoma cells
treatment: none
chip antibody: none (input)
|
| Growth protocol |
U2OS cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 DNA ligase (Enzymatics). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
120918.TI.chip.1
|
| Data processing |
Trimmed (3') sequences to 36 nts
Mapped to hg19 using bowtie -v2 -m1
Duplicates were removed with samtools rmdup
Wig coverage was calculated with IGVtools extending the reads to 200 nts
Wigs were normalized to 10,000,000 sequenced reads using a shell script
BigWigs were generated with the wigToBigWig script from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: normalized bigWigs
|
| |
|
| Submission date |
Sep 19, 2012 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE41000 |
SIRT3 functions in the nucleus in the control of stress-related gene expression. |
|
| Relations |
| SRA |
SRX188786 |
| BioSample |
SAMN01179548 |
